One goal of the Section on Drosophila Gene Regulation is to understand the regulation of homeotic gene function in Drosophila. The homeotic genes encode homeodomain-containing transcription factors that control cell fates by regulating the transcription of downstream target genes. The homeotic genes are expressed in precise spatial patterns that are crucial for the proper determination of segmental identities. The homeotic genes themselves, as well as the trans-acting factors that regulate their expression, are conserved between Drosophila and human. Understanding the regulation and function of the homeotic genes is crucial to understanding human development. Cis-acting transcriptional regulatory elements from the homeotic genes have been previously-identified by assays in transgenes in Drosophila. These assays have identified both tissue-specific enhancer elements, as well as cis-regulatory elements that are required for the maintenance of activation or repression throughout development. While these transgene assays have been important in defining the structure of the cis-regulatory elements and identifying trans-acting factors that bind them, their functions within the contexts of the endogenous genes is still not well understood. Using a transgene assay, we have identified five candidate fragments of DNA from the Sex combs reduced gene that cause transcriptional silencing of a reporter gene. These cis-regulatory silencing elements require the trans-acting proteins encoded by the Polycomb group genes. We have deleted three of these cis-regulatory silencing elements within the endogenous Sex combs reduced gene, with no discernible effects on silencing. Genetic studies first identified the Polycomb group genes by their defects in transcriptional silencing of the homeotic genes. To identify new Polycomb group genes, we have developed a transgene assay using the cis-regulatory silencing elements from the Sex combs reduced homeotic gene. Recessive mutations that disrupt transgene silencing are recovered in mitotic clones in heterozygous flies. We have screened about 98% of the genome and isolated over 300 mutants that disrupt Polycomb-dependent silencing. About one-third of these mutants are not mutations in genes that disrupt silencing, but are chromosome aberrations that generate aneuploid cells following mitotic recombination. Transgene silencing is disrupted in these cells due to changes in copy numbers of the transgene. The remaining two thirds of the mutants disrupt Polycomb-dependent silencing because they carry mutations in genes required to maintain Polycomb-dependent silencing. These mutations identify 63 genes required for Polycomb-dependent silencing, including almost all of the known Polycomb group genes. The transcription units for 44 of the 63 genes have been identified, and encode mostly DNA-binding proteins, chromatin-remodelling factors, histone-modifying enzymes, or transcription factors. Compound chromosomes have been of great use in studies of chromosome behavior during both mitosis and meiosis, but introducing genetic variants into mutant strains with compound autosomes can be difficult. We have devised and published a simplified method for easily introducing genetic variants into strains with compound autosomes. This method relies on the disjunction of non-homologous chromosomes when meiotic recombination is reduced for both the sex chromosomes and a pair of autosomes. Genetic defects that cause male infertility are common in both man and Drosophila. We have shown that mutations to male sterility in Drosophila are about 15% as common as mutations to lethality, suggesting that a substantial proportion of the Drosophila genome may be required only for male fertility. As expected from these results, we have also found that as much as 20-25% of the Drosophila proteome may be expressed only in males. The proportions of genes required for male fertility do not differ significantly between the X chromosome and the autosomes, however, translocations that exchange large portions of the X chromosome and one of the two large autosomes frequently disrupt spermatogenesis. We have generated a set of new X-autosomal translocations to test the models that have been proposed to explain this phenomenon.